GROMACS version: 2022.3
GROMACS modification: No
Dear All,
I have my protein+membrane+ligand system (as you can see in the attached figure) as a result of 500 ns of simulation with the charmm-gui protocol, but I don’t know how to remove the PBC effects, it’s the first time I’ve had a problem I have tried to correct this, but I can’t find a solution, I don’t know if you could help me with this.
Thanks.
That doesn’t look like a PBC issue to me. It seems your system was unstable and fell apart.
Yes these is an instable system, please suggest me any good parameters for protein+membrane complex with gromacs?
Geo.
You need to provide more detail about what your system is, how you prepared it, what the result of energy minimization (Epot, Fmax) was, etc.
My system is membrane(POPC)+ protein with ligand. That was prepared with charm-GUI , and protocol used was make with same given for charm-GUI . An usual error found with all systems prepared with charm GUI is LINCS error that bond o length is bad
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